Research in the Molecular Pathogenesis is focused on defining changes in the genes that underlie inherited susceptibilities to common diseases such as cancer and birth defects. Currently under investigation are the inherited breast and ovarian cancer genes, BRCA1 and BRCA2. The biological function of these proteins is currently unknown. Previously, we discovered which proteins specifically interact with BRCA1. We also have found that BRCA1 is important for controlling the expression of other genes and is plays a role in DNA repair. Recent experiments has revealed that BRCA1 appears to help in the process of recognizing and eliminating cells that may progress to form tumors. We now know that the increase in breast, ovarian and prostate cancer risk associated with genetic variants in these genes is due to a failure of these mutated proteins to function in the DNA repair pathway. We used yeast cells as an experimental model to test the functional consequences of mutations found in humans. We have also developed a system for identifying proteins that interact with BRCA1. [unreadable] [unreadable] It is also known that BRCA1 acts to transfer the protein ubiquitin onto other proteins. Through this action BRCA1 may be transferring a signal to start the DNA repair process. The identity of the protein to which this transfer occurs is unknown. We plan to identify these target proteins. We developed two systems capable of measuring this activity of BRCA1. These systems are now being used to identify specific proteins involved in breast tumor formation. During the past year we have been carrying out experiments using tagged ubiquitin expression constructs. These experiments have been successful in that we are able to follow the fate of the ubiquitin as it transferred to target proteins. To date, no BRCA1BARD1 speciific substrates have been identified. We have carried out subcellular fractionation enrich for BARD1BRCA1 fractions. These experiments have failed to enrich for ubiquitinated proteins.[unreadable] [unreadable] In the past we applied a bioinformatics approach to probe the role that genomic structure may play in protein evolution. The study of the BRCA1 and BRCA2 genes has led us to discover a new connection between a specific type of gene structure and evolutionary rates of changes. This observation appears to be generalizable to almost any gene and holds true across all metazoan lineages. We recently completed the study of all the exons in each of six genomes. The rules we observed for our smaller sample have been confirmed in this larger set.